9QED | pdb_00009qed

Cryo-EM structure of the XPF-ERCC1-SLX4(330-555)-SLX4IP complex

• PDB DOI: https://doi.org/10.2210/pdb9QED/pdb
• EM Map EMD-53055: EMDB EMDataResource

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2025-03-09 Released: 2025-12-17 
• Deposition Author(s): Feng, J., Cronin, N.B., Greber, B.J.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental, in silico

Literature

Molecular basis of XPF-ERCC1 targeting to SLX4-dependent DNA repair pathways

Feng, J., Martin, P.R., Lecot, M., Cronin, N.B., Matthews-Palmer, T., Niedzwiedz, W., Greber, B.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 214.74 kDa 
• Atom Count: 8,748 
• Modeled Residue Count: 1,088 
• Deposited Residue Count: 1,911 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein SLX4IP	A [auth C]	408	Homo sapiens	Mutation(s): 0  Gene Names: SLX4IP, C20orf94
UniProt & NIH Common Fund Data Resources
Find proteins for Q5VYV7 (Homo sapiens) Explore Q5VYV7  Go to UniProtKB:  Q5VYV7
PHAROS:  Q5VYV7 GTEx:  ENSG00000149346

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair endonuclease XPF	B [auth A]	935	Homo sapiens	Mutation(s): 0  Gene Names: ERCC4, ERCC11, XPF EC: 3.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q92889 (Homo sapiens) Explore Q92889  Go to UniProtKB:  Q92889
PHAROS:  Q92889 GTEx:  ENSG00000175595

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA excision repair protein ERCC-1	C [auth B]	297	Homo sapiens	Mutation(s): 0  Gene Names: ERCC1
UniProt & NIH Common Fund Data Resources
Find proteins for P07992 (Homo sapiens) Explore P07992  Go to UniProtKB:  P07992
PHAROS:  P07992 GTEx:  ENSG00000012061

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Structure-specific endonuclease subunit SLX4	D	271	Homo sapiens	Mutation(s): 0  Gene Names: SLX4, BTBD12, KIAA1784, KIAA1987
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IY92 (Homo sapiens) Explore Q8IY92  Go to UniProtKB:  Q8IY92
PHAROS:  Q8IY92 GTEx:  ENSG00000188827

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	4.0-beta
MODEL REFINEMENT	PHENIX	1.21rc1_4985

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-17 
Deposition Author(s): Feng, J., Cronin, N.B., Greber, B.J.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/V009354/1

Revision History  

• Version 1.0: 2025-12-17
  Type: Initial release